Judge Raymond G. Dougan, under investigation after being accused of bias in favor of defendants during 21 years on the bench, is asking the state’s highest court to prevent investigators from questioning him about how he reached individual decisions, asserting that judges should not have to reveal their inner thoughts about cases to anyone.

It is believed to be the first time in the 34-year history of the Commission on Judicial Conduct that a judge under investigation has challenged the agency’s authority, raising fears among advocates of open government and hopes among judges who believe the Dougan investigation threatens the independence of all judges.

If Dougan prevails, it could hamper future investigations into whether a Massachusetts judge is impartial on the bench.

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A lawyer for Dougan, first justice of the Boston Municipal Court division that covers much of downtown, told the Supreme Judicial Court Monday that Dougan should not have to provide notes or answer questions about his reasoning in dozens of cases the commission is reviewing for evidence that he habitually disregards evidence of guilt and hands out inappropriately light sentences to criminals.

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The broad inquiry “runs the risk of transforming a misconduct investigation into an audit of Judge Dougan’s entire career,’’ Dougan’s lawyer, Michael B. Keating, wrote in a legal brief for the hearing Monday. He said a judge’s thoughts should remain private, just like the deliberations of a jury.

But J. William Codinha, the special counsel leading the year-long investigation of Dougan, said it would set a bad precedent to allow Dougan to escape questioning. In a state where judges are appointed for life and do not have to retire until age 70, said Codinha, the commission is the only agency that can hold judges accountable for their actions.

If Dougan succeeds, “no sitting judge need ever remain truly impartial, for he may not be asked under oath if he is, and any improper bias or influence can remain safely concealed,’’ Codinha wrote in his memo to the court.

The Dougan case has sparked intense interest among other judges, many of whom contend that the investigation, following a complaint by Suffolk District Attorney Daniel F. Conley, is little more than an attempt to punish a judge whom prosecutors do not like. If the commission is allowed to question Dougan about his private thoughts on a series of cases, other judges said in friend-of-the-court briefs, then they, too, could be subjected to formal challenges by disgruntled parties.

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“All judges will be obliged to look over their shoulder as they do the work of the Commonwealth, lest someone, after the fact, bring a complaint about the ‘pattern’ their decisions seem to reflect,’’ wrote retired judges J. Owen Todd and Nancy Gertner, who wrote a brief on behalf of nine retired state and federal judges. They argue that judges should have an absolute confidentiality privilege.

Conley filed a complaint against Dougan in 2010 after years of frustration that Dougan seemed to consistently rule against prosecutors in favor of defendants, even in cases involving criminals with long rap sheets and where there was overwhelming evidence of guilt.

“I cannot stand by while a clearly biased judge ignores the law and threatens public safety,’’ Conley said in an April 2011 interview. For months, prosecutors asked Dougan to recuse himself from cases each day, arguing that he could not be fair.

A Globe review showed that, overall, prosecutors challenged Dougan’s decisions more often than those of any other sitting judge in the Boston Municipal Court system. In addition, appeals courts have reversed or modified Dougan’s decisions more than those of any other sitting judge since the mid-1990s.

In one case, Dougan dismissed drunken driving charges against Peruvian native Daniel Quispe, even though Boston police said his blood-alcohol level was twice the legal limit when he was stopped in 2000. Dougan said that he was serving “public justice’’ by dropping the charges because Quispe faced possible deportation if convicted. That, Dougan said, was too severe a penalty.

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The SJC struck down Dougan’s decision, writing that Dougan’s personal views on immigration law “are irrelevant and undermine the principle of separation of powers.’’

Defense lawyers have rushed to Dougan’s side, accusing Conley of attempting to intimidate judges who do not do what he wants. They insisted that Dougan, appointed by Governor Michael S. Dukakis, is simply “independently exercising his discretion’’ and that Conley does not like it.

To investigate Conley’s 61-page complaint, Codinha subpoenaed Dougan last November, requesting information on 30 cases in addition to those cited by Conley. Codinha said he wanted to question Dougan and requested his “notes, notebooks, bench books, diaries, memoranda, recordation, or other written recollections’’ of the cases.

Dougan balked, prompting Codinha to trim the number of additional cases covered in the subpoena to 23. But Dougan complained that investigators were asking for too much information with too little explanation for why they want it.

On Monday Dougan’s lawyer, Keating, asked the court to limit or throw out Codinha’s subpoena altogether. He said he wanted the court to recognize that judges enjoy a “judicial deliberations privilege’’ exempting them from answering questions beyond the public record about decisions.

Otherwise, Keating said, disclosure of Dougan’s thoughts would invite lawyers to look for doubts and flaws in past rulings, undercutting the decisions.

“New explanations of old decisions have the potential . . . to undermine the public’s confidence in the judiciary,’’ Keating wrote.

But Codinha said that the commission’s work is done primarily in secret. Dougan’s name was never mentioned in the court hearing, and it was blacked out in documents. In addition, any questioning of Dougan would be done confidentially, not in open court.

Robert A. Barton, a retired superior court judge who chaired the commission in the 1990s, said he could not remember any other time a judge challenged the authority of the commission before an appeals court.

But Dougan has raised an important issue, Barton said. “It’s an issue that should be resolved by a court. If I were Dougan, I would do the same thing.’’

On the other side, former Bristol district attorney Paul F. Walsh said judges must be held accountable, as is everyone else in government.

“This is probably the best, most confidential internal disciplinary proceeding that protects the prerogative of judges while allowing for accountability,’’ said Walsh, now a lawyer in private practice. “Nobody likes to be held accountable. But that accountability breeds the public’s faith in what you do.’’